NM_000070.3(CAPN3):c.984C>T (p.Cys328=) AND Limb-girdle muscular dystrophy, type 2A

Clinical significance:Benign/Likely benign (Last evaluated: Dec 5, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000538067.7

Allele description [Variation Report for NM_000070.3(CAPN3):c.984C>T (p.Cys328=)]

NM_000070.3(CAPN3):c.984C>T (p.Cys328=)

Gene:
CAPN3:calpain 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q15.1
Genomic location:
Preferred name:
NM_000070.3(CAPN3):c.984C>T (p.Cys328=)
HGVS:
  • NC_000015.10:g.42392677C>T
  • NG_008660.1:g.49575C>T
  • NM_000070.3:c.984C>TMANE SELECT
  • NM_024344.1:c.984C>T
  • NM_173087.1:c.840C>T
  • NP_000061.1:p.Cys328=
  • NP_077320.1:p.Cys328=
  • NP_775110.1:p.Cys280=
  • LRG_849t1:c.984C>T
  • LRG_849:g.49575C>T
  • LRG_849p1:p.Cys328=
  • NC_000015.9:g.42684875C>T
  • NM_000070.2:c.984C>T
  • NP_000061.1:p.(=)
  • NP_000061.1:p.(=)
Links:
dbSNP: rs28364441
NCBI 1000 Genomes Browser:
rs28364441
Molecular consequence:
  • NM_000070.3:c.984C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_024344.1:c.984C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_173087.1:c.840C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Limb-girdle muscular dystrophy, type 2A (LGMDR1)
Synonyms:
Limb-girdle muscular dystrophy type 2; Muscular dystrophy, pelvofemoral; Leyden-Moebius muscular dystrophy; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009675; MedGen: C1869123; Orphanet: 267; OMIM: 253600

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000645521Invitaecriteria provided, single submitter
Benign
(Dec 5, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001277568Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Apr 27, 2017)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV001454332Natera, Inc.no assertion criteria providedBenign
(Sep 16, 2020)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Correlations between clinical severity, genotype and muscle pathology in limb girdle muscular dystrophy type 2A.

Fanin M, Nardetto L, Nascimbeni AC, Tasca E, Spinazzi M, Padoan R, Angelini C.

J Med Genet. 2007 Oct;44(10):609-14. Epub 2007 May 25.

PubMed [citation]
PMID:
17526799
PMCID:
PMC2597960
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000645521.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV001277568.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001454332.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 18, 2021

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